Contacts of the helix formed by residues 2254 - 2263 (chain H) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS2254 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209H MET* 3.8 32.3 - - + -
2250H SER 5.0 0.2 + - - -
2251H MET* 3.3 12.7 + - + +
2252H PHE 3.2 1.6 - - - -
2253H ASP* 1.3 75.3 - - + +
2255H LEU* 1.3 58.5 + - - +
2256H SER* 3.3 3.4 - - - -
2257H TYR* 3.4 11.4 + - + +
2258H LEU* 2.9 34.5 + - + +
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Residues in contact with LEU2255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251H MET 4.3 0.8 + - - -
2252H PHE* 3.2 44.9 + - + +
2253H ASP 3.3 1.2 - - - -
2254H HIS* 1.3 77.2 - - - +
2256H SER* 1.3 58.2 + - - +
2258H LEU* 3.3 7.2 + - + +
2259H LEU* 2.9 30.4 + - + +
2277H ALA* 3.9 26.5 - - + -
2280H SER* 4.1 14.1 - - - +
2281H VAL* 4.2 15.3 - - + -
2291H LEU* 3.7 22.7 - - + -
2295H ASP* 4.7 14.1 - - + -
2335H PHE* 4.6 8.3 - - + -
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Residues in contact with SER2256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2253H ASP 4.3 9.8 + - - -
2254H HIS* 4.7 0.3 - - - -
2255H LEU* 1.3 77.8 - - - +
2257H TYR* 1.3 58.4 + - - +
2259H LEU* 3.3 6.1 + - - +
2260H GLU* 2.9 29.0 + - - +
2295H ASP* 5.5 6.1 - - - -
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Residues in contact with TYR2257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209H MET* 4.2 25.6 - - - -
2212H MET* 4.7 9.4 - - + -
2213H VAL* 3.2 38.3 - - + +
2216H LEU* 5.2 1.6 - - - +
2254H HIS* 3.4 13.3 + - + +
2255H LEU 3.3 0.4 - - - -
2256H SER* 1.3 81.4 + - - +
2258H LEU* 1.3 61.0 + - + +
2260H GLU* 3.3 7.0 + - + +
2261H ASN* 2.9 70.1 + - + +
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Residues in contact with LEU2258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209H MET* 4.9 4.7 - - + -
2212H MET* 3.9 24.7 - - + -
2237H LEU* 5.3 1.6 - - + -
2251H MET* 4.0 18.4 - - + +
2254H HIS* 2.9 26.6 + - + +
2255H LEU* 3.7 7.6 - - - +
2257H TYR* 1.3 79.0 - - + +
2259H LEU* 1.3 56.5 + - - +
2261H ASN* 3.4 4.9 + - + +
2262H SER* 2.9 31.1 + - - -
2273H PRO* 3.8 33.1 - - + +
2276H VAL* 3.8 29.6 - - + -
2277H ALA* 4.4 16.8 - - + +
2280H SER* 5.2 2.9 - - - +
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Residues in contact with LEU2259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255H LEU* 2.9 21.4 + - + +
2256H SER* 3.8 3.8 - - - +
2258H LEU* 1.3 76.2 - - - +
2260H GLU* 1.3 61.9 + - - +
2262H SER* 2.7 20.5 + - - -
2263H GLY 3.7 4.3 + - - -
2277H ALA* 5.4 0.6 - - - +
2295H ASP* 4.5 25.4 - - + +
2298H LYS* 5.5 6.5 - - + -
2299H VAL* 6.1 3.1 - - + -
2302H TYR* 3.7 13.7 - - + -
2335H PHE* 5.8 6.3 - - + -
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Residues in contact with GLU2260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2256H SER 2.9 17.4 + - - +
2257H TYR* 3.7 11.4 - - + +
2259H LEU* 1.3 79.0 - - - +
2261H ASN* 1.3 65.5 + - - +
2263H GLY* 3.8 8.5 + - - -
2302H TYR* 4.4 12.4 + - - +
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Residues in contact with ASN2261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212H MET* 5.5 3.5 - - + +
2216H LEU* 3.5 35.7 - - + +
2257H TYR* 2.9 66.7 + - + +
2258H LEU* 4.0 5.2 - - + +
2260H GLU* 1.3 79.1 - - - +
2262H SER* 1.3 65.2 + - - +
2263H GLY* 3.5 0.5 + - - -
2273H PRO* 4.7 11.4 - - + +
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Residues in contact with SER2262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2258H LEU 2.9 15.6 + - - -
2259H LEU* 2.7 28.1 + - - -
2261H ASN* 1.3 77.9 - - - +
2263H GLY* 1.3 66.1 + - - +
2272H THR* 5.2 5.5 - - - +
2273H PRO* 4.4 8.3 - - - +
2274H LEU* 3.9 40.9 - - - +
2302H TYR* 5.2 0.9 - - - -
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Residues in contact with GLY2263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259H LEU 3.7 5.1 + - - -
2260H GLU 3.8 5.3 + - - -
2261H ASN 3.3 3.0 - - - -
2262H SER* 1.3 90.1 + - - +
2274H LEU* 5.6 2.4 - - - +
2299H VAL* 6.1 0.5 - - - +
2302H TYR* 3.3 51.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il